Objective: We aimed to develop a user-friendly image-analysis pipeline to simultaneously generate perfusion andventilation maps derived from Fourier decomposition of free-breathing pulmonary 1~H magnetic resonance imaging(FDMRI).Methods: Free-breathing 1~H MR images were non-rigidly deformed to a 1~H reference image selected halfwaybetween inspiration and expiration, using modality independent neighbourhood descriptor-based registration. The 1~Hreference image was segmented using multi-region coupled continuous max-flow. The co-registered image sequencewas Fourier transformed on a voxel-by-voxel basis to generate images of the voxel-wise power spectrum. The twolargest intensity peaks in the power spectrum corresponded to respiratory and cardiac frequencies, which were usedto generate ventilation and perfusion maps, respectively. Perfusion and ventilation defects were measured using fuzzyc-means clustering in 15 asthmatics who provided written-informed-consent to pulmonary function tests and MRI.Results: The proposed FDMRI pipeline was used to generate perfusion maps in 15 asthma patients for directcomparison with 3~He and FDMRI ventilation maps. FDMRI perfusion measurements were significantly correlatedwith FDMRI (r~2=0.48, p=0.03) and 3~He MRI ventilation (r~2=0.44, p=0.05).Conclusion: Ventilation and perfusion free-breathing 1~H MRI maps were generated in asthmatics with clinicallyacceptableaccuracy and minimal user interaction using a pipeline compatible with high throughput clinicalworkflows.
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